Scientific Question: Given the significant reduction for the risk of breast cancer after obese patients undergo bariatric surgery, what specific genes are responsible for the reduced risk and how do the expression levels of these certain genes change after the surgery?

Hypothesis: If the levels of Estrogen Receptor Alpha decrease after bariatric surgery, then by analyzing the specific gene (ESR1) expression levels of this protein and associated pathways will show a marked change from pre-weight loss surgery levels that are responsible for the preventative phenotype against breast cancer.

The packages Edger and limma are used to filter out lowly expressed counts and to model the voom plot in RNA-seq and also EdgeR is used in Pathway analysis to gain access to cerrtain functions

library(edgeR)
## Loading required package: limma
library(limma)

The package msa used to align multiple sequences from a single fasta file with its function msa

library(msa)
## Loading required package: Biostrings
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following object is masked from 'package:limma':
## 
##     plotMA
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
##     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
##     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
##     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
##     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which.max, which.min
## Loading required package: S4Vectors
## Loading required package: stats4
## 
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## Loading required package: IRanges
## Loading required package: XVector
## Loading required package: GenomeInfoDb
## 
## Attaching package: 'Biostrings'
## The following object is masked from 'package:base':
## 
##     strsplit
seqdata<- read.csv("/Users/heatherotto/Downloads/GSE126803_AI007_Readcounts.csv")
seqdata
dim(seqdata)
## [1] 19645    61
countdata<- seqdata[,-(1)]
countdata
rownames(countdata) <- seqdata[,1]
head(countdata)
sampleinfo<- read.delim("/Users/heatherotto/Sampleinfo copy.txt", row.names= NULL)
colnames(sampleinfo) <- colnames(sampleinfo)[2:ncol(sampleinfo)]
sampleinfo
sampleinfo<- sampleinfo[, -(3:4)]
sampleinfo
y<- DGEList(countdata)
y
## An object of class "DGEList"
## $counts
##         AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST
## DEPDC1B     0.08969942      0.1377730      0.4689322      0.6425727
## CLASP1      8.29223807      6.9066242     10.0749860      9.0827100
## TSC2       20.41821708     20.9614251     14.6790392     21.8024361
## ERGIC2     24.29453789     31.6844127     36.8340772     33.1361719
## SPG20OS     0.51340170      0.4293197      0.0000000      0.0677277
##         AI007_P40_POST AI007_P43_POST AI007_P62_POST AI007_P64_POST
## DEPDC1B      0.2710652      0.2390679      0.3810158     0.02985079
## CLASP1      12.9326915      8.8306438      8.5018542     7.41074318
## TSC2        22.7280129     17.6134194     20.5334382    22.90115266
## ERGIC2      33.7938411     34.6500575     28.0519829    19.67938260
## SPG20OS      0.8594560      0.3434817      0.3375794     0.65612606
##         AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
## DEPDC1B      0.3991934     0.04679104       0.000000      0.1567836
## CLASP1       9.2111196     8.82339225       8.252884      8.5378324
## TSC2        17.9478907    27.03462975      18.732465     16.9429477
## ERGIC2      25.6030502    25.31411789      27.274788     31.6587906
## SPG20OS      0.4714289     0.38284594       0.000000      0.3943235
##         AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST
## DEPDC1B      0.0501999     0.09899953     0.06860305      0.1752291
## CLASP1       8.8948742    11.14349889     9.53456943      9.2975701
## TSC2        22.7482431    18.68817115    14.17456014     21.7803833
## ERGIC2      27.6848779    25.12473641    33.27308743     40.7538765
## SPG20OS      0.7444397     0.32698846     0.08126292      0.0000000
##         AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST
## DEPDC1B     0.09320857     0.04430422      0.3536386      0.1603581
## CLASP1      8.20042424     8.39604851      9.6874216     11.2414363
## TSC2       16.24760807    16.16759857     16.2564699     16.5288894
## ERGIC2     29.55974952    29.14257278     34.8356066     36.1047479
## SPG20OS     0.15388827     0.35194182      1.1519228      0.1827098
##         AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST
## DEPDC1B    0.02380131    0.09098328     0.13393686     0.06969021
## CLASP1     4.81093742    8.95276389     9.40307322     8.58215847
## TSC2      11.98917274   18.41631154    21.51137553    15.50351101
## ERGIC2    17.25532438   31.16564676    38.77159560    34.22509806
## SPG20OS    0.37986174    0.05784366     0.05784366     0.42124056
##         AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
## DEPDC1B     0.03364489     0.4911890      0.3610493      0.1136028
## CLASP1      6.31334240     8.8250530     11.4324839      8.2329628
## TSC2       15.23328212    14.4110359     19.3913762     19.0121881
## ERGIC2     36.16802991    40.6769330     16.2188413     32.0814595
## SPG20OS     0.28019428     0.4795911      0.1835943      0.3755042
##         AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE
## DEPDC1B     0.09291356    0.01116544       0.00000    0.05779537    0.19430432
## CLASP1      7.89373506   11.08134880      12.52725   10.05180875   12.04448929
## TSC2       19.86529843   19.42022476      23.86788   25.82734610   14.85757132
## ERGIC2     36.98349010   28.48121922      24.21277   27.16994391   31.08928686
## SPG20OS     0.05213495    1.56143639       0.00000    0.29807249    0.09558827
##         AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE
## DEPDC1B     0.2393998     0.1357762    0.06355554    0.02536228     0.1194512
## CLASP1      8.6591094     8.3761595    9.35402683    5.99278228     9.2258454
## TSC2       15.4644994    14.3929859   22.85739826   32.78989079    16.0272630
## ERGIC2     36.3008713    27.5867316   52.14664520   15.80894345    33.7884990
## SPG20OS     0.1267672     0.0000000    0.39923433    0.30728566     0.0000000
##         AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE
## DEPDC1B     0.1759087    0.03254789    0.07536732     0.1879747    0.07500112
## CLASP1      8.6915694    8.59145698    8.92918670    10.2306575    7.69298607
## TSC2       23.8790380   19.74323945   20.30813567    19.6965824   17.38359714
## ERGIC2     25.5698107   24.17770466   31.09084848    35.7840620   23.88359358
## SPG20OS     1.2991460    0.06013589    0.09353621     0.1749615    0.09183099
##         AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE
## DEPDC1B    0.23588178    0.22121742    0.24536749    0.03151935    0.02822746
## CLASP1     4.63658607   10.72337215    8.79752802   11.58481344   10.31491832
## TSC2      28.39474488   20.30840905   15.84455339   18.91443947   16.63015918
## ERGIC2     9.94057162   21.77228556   34.61117909   25.76242226   33.89741809
## SPG20OS    0.08263845    0.07534792    0.07605192    0.80623522    0.34338226
##         AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
## DEPDC1B     0.2077901   0.09047029 9.650265e-04     0.3415222     0.2326068
## CLASP1      9.7284928   9.38149203 7.210589e+00    11.0368002     6.2912171
## TSC2       19.3889038  17.18876511 1.596532e+01    14.3247503    27.8789860
## ERGIC2     29.5176014  31.56035801 2.612456e+01    30.6970516    18.1402925
## SPG20OS     0.4916952   0.80873645 5.784366e-02     0.2776951     0.1834748
##         AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE
## DEPDC1B    0.36919153    0.1681029    0.05386508    0.01116544    0.16008039
## CLASP1    11.24710885    8.8419275   12.24037933   11.55106685    8.44684402
## TSC2      22.02743093   22.4983255   14.26515557   28.16410194   18.75746435
## ERGIC2    26.32010071   29.1152262   35.10153190   31.64211155   35.30127013
## SPG20OS    0.05784366    0.1847546    0.19649589    0.47239067    0.05213495
##         AI007_P58_PRE AI007_P5_PRE
## DEPDC1B     0.2963357   0.01116544
## CLASP1      6.7596874   8.82584809
## TSC2       23.1045227  17.81352521
## ERGIC2     23.5141753  28.86583911
## SPG20OS     0.4902792   0.05213495
## 19640 more rows ...
## 
## $samples
##                group lib.size norm.factors
## AI007_P45_POST     1 651502.0            1
## AI007_P42_POST     1 744900.4            1
## AI007_P41_POST     1 603802.9            1
## AI007_P44_POST     1 626656.8            1
## AI007_P40_POST     1 607903.6            1
## 55 more rows ...
group<- paste(sampleinfo$Surgery.Status, sep= ".")
group
##  [1] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
##  [7] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
## [13] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
## [19] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
## [25] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
## [31] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
## [37] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
## [43] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
## [49] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
## [55] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"
group<- factor(group)
group
##  [1]   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s
##  [9]   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s
## [17]   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s
## [25]   post.s   post.s   post.s   post.s   post.s   post.s   pre.s    pre.s 
## [33]   pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s 
## [41]   pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s 
## [49]   pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s 
## [57]   pre.s    pre.s    pre.s    pre.s 
## Levels:   post.s   pre.s
y$samples$group<- group
y$samples
CPM<- cpm(countdata)
head(CPM)
##         AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST
## DEPDC1B      0.1376810       0.184955      0.7766311      1.0253981
## CLASP1      12.7278790       9.271876     16.6858846     14.4939145
## TSC2        31.3402237      28.139903     24.3109770     34.7916695
## ERGIC2      37.2900458      42.535099     61.0034754     52.8777032
## SPG20OS      0.7880279       0.576345      0.0000000      0.1080778
## HLX          9.9572347       9.841279     19.1784913      6.9123182
##         AI007_P40_POST AI007_P43_POST AI007_P62_POST AI007_P64_POST
## DEPDC1B      0.4459015      0.3555442      0.6073717     0.04975775
## CLASP1      21.2742457     13.1330206     13.5526799    12.35283775
## TSC2        37.3875254     26.1948512     32.7320500    38.17352944
## ERGIC2      55.5907855     51.5319075     44.7172508    32.80321746
## SPG20OS      1.4138030      0.5108293      0.5381304     1.09368501
## HLX         14.0398512      5.4306752      6.2637551    11.17865870
##         AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
## DEPDC1B      0.6134787     0.07298751        0.00000      0.2487687
## CLASP1      14.1556083    13.76326557       13.13182     13.5469914
## TSC2        27.5822399    42.17026495       29.80672     26.8834005
## ERGIC2      39.3466555    39.48650557       43.39909     50.2330503
## SPG20OS      0.7244898     0.59718645        0.00000      0.6256736
## HLX          7.8712893     9.16736771       14.37628     16.5960244
##         AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST
## DEPDC1B     0.07689474      0.1507720     0.09786017      0.2619113
## CLASP1     13.62490813     16.9710611    13.60077467     13.8968860
## TSC2       34.84509333     28.4612667    20.21958098     32.5546891
## ERGIC2     42.40688611     38.2638739    47.46305203     60.9139775
## SPG20OS     1.14031090      0.4979891     0.11591909      0.0000000
## HLX        12.51026812      9.9915607     9.51009805      6.5911767
##         AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST
## DEPDC1B      0.1575402     0.06453105      0.5359515      0.2541925
## CLASP1      13.8602742    12.22921493     14.6816209     17.8194199
## TSC2        27.4615431    23.54882032     24.6372396     26.2008531
## ERGIC2      49.9615901    42.44744246     52.7945608     57.2316248
## SPG20OS      0.2601004     0.51261878      1.7457787      0.2896233
## HLX         16.6818535     9.58529041      7.6478274     16.6786706
##         AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST
## DEPDC1B    0.03687605    0.12318349     0.19023079      0.1071199
## CLASP1     7.45372347   12.12126812    13.35520409     13.1915221
## TSC2      18.57516955   24.93409328    30.55265058     23.8302414
## ERGIC2    26.73416947   42.19559069    55.06737638     52.6069447
## SPG20OS    0.58853070    0.07831531     0.08215546      0.6474833
## HLX        8.02720308   11.32261966    13.50681928     10.7993960
##         AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
## DEPDC1B     0.04977093     0.7653514      0.5558158      0.1740532
## CLASP1      9.33933450    13.7508529     17.5996884     12.6138910
## TSC2       22.53461135    22.4547134     29.8519711     29.1289630
## ERGIC2     53.50340727    63.3812084     24.9680258     49.1526615
## SPG20OS     0.41449171     0.7472800      0.2826335      0.5753177
## HLX         7.80634047     5.8293813     14.4568159     11.9185654
##         AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE
## DEPDC1B     0.15371699    0.01438479       0.00000    0.08903184     0.3333328
## CLASP1     13.05946325   14.27644892      19.81262   15.48447534    20.6625532
## TSC2       32.86532077   25.01968414      37.74851   39.78616320    25.4884495
## ERGIC2     61.18580445   36.69324724      38.29398   41.85439024    53.3342700
## SPG20OS     0.08625252    2.01164743       0.00000    0.45917070     0.1639835
## HLX         8.91259009   10.87532853      12.23494   11.41288168    17.4088069
##         AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE
## DEPDC1B     0.3947641     0.2043082    0.09667073    0.03777452     0.1960563
## CLASP1     14.2786513    12.6039606   14.22788015    8.92563489    15.1424610
## TSC2       25.5005665    21.6577332   34.76709325   48.83718109    26.3056873
## ERGIC2     59.8592141    41.5109191   79.31730708   23.54580072    55.4573597
## SPG20OS     0.2090360     0.0000000    0.60725272    0.45767049     0.0000000
## HLX        12.6010172    10.0983550    6.03572098   15.45410992    10.6818107
##         AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE
## DEPDC1B     0.3068482    0.05408842     0.1239154     0.3031964     0.1099199
## CLASP1     15.1612252   14.27737042    14.6809426    16.5016818    11.2746586
## TSC2       41.6536366   32.80951573    33.3896675    31.7698775    25.4769891
## ERGIC2     44.6029527   40.17875502    51.1180893    57.7184021    35.0032303
## SPG20OS     2.2661783    0.09993444     0.1537878     0.2822066     0.1345853
## HLX         8.5080819   10.53306579    18.4490750     8.6836860    11.6405492
##         AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE
## DEPDC1B     0.3931737     0.3679884     0.3869206    0.05036387    0.04245563
## CLASP1      7.7283789    17.8379990    13.8728423   18.51104419   15.51419290
## TSC2       47.3290790    33.7824125    24.9853128   30.22284533   25.01265542
## ERGIC2     16.5691962    36.2175259    54.5784482   41.16504244   50.98354316
## SPG20OS     0.1377439     0.1253389     0.1199264    1.28826035    0.51646543
## HLX         5.8029265     7.0288823    15.7095021   10.73029358   17.32316123
##         AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
## DEPDC1B     0.3515309    0.1448049  0.001221554     0.5517809     0.3788969
## CLASP1     16.4582718   15.0158282  9.127337396    17.8316263    10.2478628
## TSC2       32.8013656   27.5119932 20.209282551    23.1438088    45.4125204
## ERGIC2     49.9366880   50.5148769 33.069097494    49.5957469    29.5490089
## SPG20OS     0.8318301    1.2944474  0.073219893     0.4486587     0.2988650
## HLX        14.3502361    3.7544269  9.520771392    13.0328029     8.2901708
##         AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE
## DEPDC1B    0.58057106    0.2821525    0.08606747    0.01869908    0.25238204
## CLASP1    17.68660801   14.8407452   19.55809704   19.34489523   13.31725704
## TSC2      34.63917185   37.7623452   22.79335381   47.16721045   29.57293557
## ERGIC2    41.38959712   48.8684912   56.08642907   52.99193057   55.65582680
## SPG20OS    0.09096187    0.3101016    0.31396785    0.79112588    0.08219574
## HLX        6.84981814   13.4309882   11.45157177   13.50679998    6.81095190
##         AI007_P58_PRE AI007_P5_PRE
## DEPDC1B     0.4132298   0.01415905
## CLASP1      9.4261484  11.19217670
## TSC2       32.2184511  22.58957098
## ERGIC2     32.7896973  36.60515893
## SPG20OS     0.6836773   0.06611304
## HLX         7.2381350  15.63307167
plot(CPM[,1], countdata[,1], ylim= c(0,50), xlim= c(0,30))
abline(v= 18)

thresh<- CPM > 18
head(thresh)
##         AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST
## DEPDC1B          FALSE          FALSE          FALSE          FALSE
## CLASP1           FALSE          FALSE          FALSE          FALSE
## TSC2              TRUE           TRUE           TRUE           TRUE
## ERGIC2            TRUE           TRUE           TRUE           TRUE
## SPG20OS          FALSE          FALSE          FALSE          FALSE
## HLX              FALSE          FALSE           TRUE          FALSE
##         AI007_P40_POST AI007_P43_POST AI007_P62_POST AI007_P64_POST
## DEPDC1B          FALSE          FALSE          FALSE          FALSE
## CLASP1            TRUE          FALSE          FALSE          FALSE
## TSC2              TRUE           TRUE           TRUE           TRUE
## ERGIC2            TRUE           TRUE           TRUE           TRUE
## SPG20OS          FALSE          FALSE          FALSE          FALSE
## HLX              FALSE          FALSE          FALSE          FALSE
##         AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
## DEPDC1B          FALSE          FALSE          FALSE          FALSE
## CLASP1           FALSE          FALSE          FALSE          FALSE
## TSC2              TRUE           TRUE           TRUE           TRUE
## ERGIC2            TRUE           TRUE           TRUE           TRUE
## SPG20OS          FALSE          FALSE          FALSE          FALSE
## HLX              FALSE          FALSE          FALSE          FALSE
##         AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST
## DEPDC1B          FALSE          FALSE          FALSE          FALSE
## CLASP1           FALSE          FALSE          FALSE          FALSE
## TSC2              TRUE           TRUE           TRUE           TRUE
## ERGIC2            TRUE           TRUE           TRUE           TRUE
## SPG20OS          FALSE          FALSE          FALSE          FALSE
## HLX              FALSE          FALSE          FALSE          FALSE
##         AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST
## DEPDC1B          FALSE          FALSE          FALSE          FALSE
## CLASP1           FALSE          FALSE          FALSE          FALSE
## TSC2              TRUE           TRUE           TRUE           TRUE
## ERGIC2            TRUE           TRUE           TRUE           TRUE
## SPG20OS          FALSE          FALSE          FALSE          FALSE
## HLX              FALSE          FALSE          FALSE          FALSE
##         AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST
## DEPDC1B         FALSE         FALSE          FALSE          FALSE
## CLASP1          FALSE         FALSE          FALSE          FALSE
## TSC2             TRUE          TRUE           TRUE           TRUE
## ERGIC2           TRUE          TRUE           TRUE           TRUE
## SPG20OS         FALSE         FALSE          FALSE          FALSE
## HLX             FALSE         FALSE          FALSE          FALSE
##         AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
## DEPDC1B          FALSE         FALSE          FALSE          FALSE
## CLASP1           FALSE         FALSE          FALSE          FALSE
## TSC2              TRUE          TRUE           TRUE           TRUE
## ERGIC2            TRUE          TRUE           TRUE           TRUE
## SPG20OS          FALSE         FALSE          FALSE          FALSE
## HLX              FALSE         FALSE          FALSE          FALSE
##         AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE
## DEPDC1B          FALSE         FALSE         FALSE         FALSE         FALSE
## CLASP1           FALSE         FALSE          TRUE         FALSE          TRUE
## TSC2              TRUE          TRUE          TRUE          TRUE          TRUE
## ERGIC2            TRUE          TRUE          TRUE          TRUE          TRUE
## SPG20OS          FALSE         FALSE         FALSE         FALSE         FALSE
## HLX              FALSE         FALSE         FALSE         FALSE         FALSE
##         AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE
## DEPDC1B         FALSE         FALSE         FALSE         FALSE         FALSE
## CLASP1          FALSE         FALSE         FALSE         FALSE         FALSE
## TSC2             TRUE          TRUE          TRUE          TRUE          TRUE
## ERGIC2           TRUE          TRUE          TRUE          TRUE          TRUE
## SPG20OS         FALSE         FALSE         FALSE         FALSE         FALSE
## HLX             FALSE         FALSE         FALSE         FALSE         FALSE
##         AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE
## DEPDC1B         FALSE         FALSE         FALSE         FALSE         FALSE
## CLASP1          FALSE         FALSE         FALSE         FALSE         FALSE
## TSC2             TRUE          TRUE          TRUE          TRUE          TRUE
## ERGIC2           TRUE          TRUE          TRUE          TRUE          TRUE
## SPG20OS         FALSE         FALSE         FALSE         FALSE         FALSE
## HLX             FALSE         FALSE          TRUE         FALSE         FALSE
##         AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE
## DEPDC1B         FALSE         FALSE         FALSE         FALSE         FALSE
## CLASP1          FALSE         FALSE         FALSE          TRUE         FALSE
## TSC2             TRUE          TRUE          TRUE          TRUE          TRUE
## ERGIC2          FALSE          TRUE          TRUE          TRUE          TRUE
## SPG20OS         FALSE         FALSE         FALSE         FALSE         FALSE
## HLX             FALSE         FALSE         FALSE         FALSE         FALSE
##         AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
## DEPDC1B         FALSE        FALSE        FALSE         FALSE         FALSE
## CLASP1          FALSE        FALSE        FALSE         FALSE         FALSE
## TSC2             TRUE         TRUE         TRUE          TRUE          TRUE
## ERGIC2           TRUE         TRUE         TRUE          TRUE          TRUE
## SPG20OS         FALSE        FALSE        FALSE         FALSE         FALSE
## HLX             FALSE        FALSE        FALSE         FALSE         FALSE
##         AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE
## DEPDC1B         FALSE        FALSE         FALSE         FALSE         FALSE
## CLASP1          FALSE        FALSE          TRUE          TRUE         FALSE
## TSC2             TRUE         TRUE          TRUE          TRUE          TRUE
## ERGIC2           TRUE         TRUE          TRUE          TRUE          TRUE
## SPG20OS         FALSE        FALSE         FALSE         FALSE         FALSE
## HLX             FALSE        FALSE         FALSE         FALSE         FALSE
##         AI007_P58_PRE AI007_P5_PRE
## DEPDC1B         FALSE        FALSE
## CLASP1          FALSE        FALSE
## TSC2             TRUE         TRUE
## ERGIC2           TRUE         TRUE
## SPG20OS         FALSE        FALSE
## HLX             FALSE        FALSE
table(rowSums(thresh))
## 
##     0     1     2     3     4     5     6     7     8     9    10    11    12 
## 11088   414   301   212   177   120   136   126    96    85    88    83    79 
##    13    14    15    16    17    18    19    20    21    22    23    24    25 
##    66    61    51    51    75    72    59    76    58    67    56    47    51 
##    26    27    28    29    30    31    32    33    34    35    36    37    38 
##    41    57    54    56    59    58    43    55    56    48    62    48    64 
##    39    40    41    42    43    44    45    46    47    48    49    50    51 
##    43    55    56    63    50    64    61    69    68    73    72    74    99 
##    52    53    54    55    56    57    58    59    60 
##    99   122   116   146   184   181   251   405  2798
keep<- rowSums(thresh) >= 2
summary(keep)
##    Mode   FALSE    TRUE 
## logical   11502    8143
y <- y[keep,keep.lib.size=FALSE]
y<- calcNormFactors(y)
y
## An object of class "DGEList"
## $counts
##        AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST
## CLASP1       8.292238       6.906624      10.074986       9.082710
## TSC2        20.418217      20.961425      14.679039      21.802436
## ERGIC2      24.294538      31.684413      36.834077      33.136172
## HLX          6.487158       7.330773      11.580029       4.331651
## CP          11.511853      25.831897       6.207498       5.939641
##        AI007_P40_POST AI007_P43_POST AI007_P62_POST AI007_P64_POST
## CLASP1      12.932691       8.830644       8.501854       7.410743
## TSC2        22.728013      17.613419      20.533438      22.901153
## ERGIC2      33.793841      34.650058      28.051983      19.679383
## HLX          8.534877       3.651586       3.929373       6.706327
## CP           2.835163      30.697666       0.000000       4.533726
##        AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
## CLASP1       9.211120       8.823392      8.2528837       8.537832
## TSC2        17.947891      27.034630     18.7324655      16.942948
## ERGIC2      25.603050      25.314118     27.2747882      31.658791
## HLX          5.121884       5.877041      9.0349844      10.459450
## CP          11.995819      15.971785      0.2165844       0.000000
##        AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST
## CLASP1       8.894874      11.143499       9.534569       9.297570
## TSC2        22.748243      18.688171      14.174560      21.780383
## ERGIC2      27.684878      25.124736      33.273087      40.753877
## HLX          8.167194       6.560635       6.666877       4.409760
## CP           9.457096       8.434184       1.926218       7.186049
##        AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST
## CLASP1       8.200424     8.39604851       9.687422      11.241436
## TSC2        16.247608    16.16759857      16.256470      16.528889
## ERGIC2      29.559750    29.14257278      34.835607      36.104748
## HLX          9.869810     6.58084462       5.046291      10.521791
## CP           5.628690     0.05368532      10.312428       9.599091
##        AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
## CLASP1      4.810937      8.952764       9.403073       8.582158       6.313342
## TSC2       11.989173     18.416312      21.511376      15.503511      15.233282
## ERGIC2     17.255324     31.165647      38.771596      34.225098      36.168030
## HLX         5.181085      8.362882       9.509822       7.025886       5.277046
## CP         10.747973      9.636731       8.296421       7.785506       9.009380
##        AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST
## CLASP1      8.825053      11.432484       8.232963       7.893735     11.081349
## TSC2       14.411036      19.391376      19.012188      19.865298     19.420225
## ERGIC2     40.676933      16.218841      32.081459      36.983490     28.481219
## HLX         3.741193       9.390923       7.779131       5.387176      8.441407
## CP          1.378040       5.245250      12.632921      22.889810     10.502402
##        AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE
## CLASP1     12.527255     10.051809      12.04449      8.659109      8.376159
## TSC2       23.867881     25.827346      14.85757     15.464499     14.392986
## ERGIC2     24.212771     27.169944      31.08929     36.300871     27.586732
## HLX         7.735992      7.408718      10.14784      7.641729      6.711020
## CP         10.242538     20.321663      16.69494     18.587691      4.962621
##        AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE AI007_P56_PRE
## CLASP1      9.354027      5.992782      9.225845      8.691569     8.5914570
## TSC2       22.857398     32.789891     16.027263     23.879038    19.7432395
## ERGIC2     52.146645     15.808943     33.788499     25.569811    24.1777047
## HLX         3.968145     10.376082      6.508106      4.877481     6.3383087
## CP          7.048288      0.000000      4.897516     20.190741     0.2995237
##        AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE
## CLASP1      8.929187     10.230658      7.692986      4.636586    10.7233721
## TSC2       20.308136     19.696582     17.383597     28.394745    20.3084091
## ERGIC2     31.090848     35.784062     23.883594      9.940572    21.7722856
## HLX        11.221026      5.383683      7.942643      3.481425     4.2254358
## CP          1.952987      6.241647     16.296264      0.000000     0.3450054
##        AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE
## CLASP1      8.797528     11.584813      10.31492      9.728493     9.381492
## TSC2       15.844553     18.914439      16.63016     19.388904    17.188765
## ERGIC2     34.611179     25.762422      33.89742     29.517601    31.560358
## HLX         9.962254      6.715367      11.51765      8.482432     2.345667
## CP         15.404036      5.236207       5.01858     12.467803    78.443385
##        AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE AI007_P17_PRE AI007_P1_PRE
## CLASP1     7.210589     11.036800      6.291217     11.247109     8.841927
## TSC2      15.965317     14.324750     27.878986     22.027431    22.498326
## ERGIC2    26.124560     30.697052     18.140293     26.320101    29.115226
## HLX        7.521402      8.066591      5.089380      4.355875     8.002012
## CP        12.113838      7.752517      6.637065      7.552611     3.457671
##        AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
## CLASP1     12.240379     11.551067      8.446844      6.759687     8.825848
## TSC2       14.265156     28.164102     18.757464     23.104523    17.813525
## ERGIC2     35.101532     31.642112     35.301270     23.514175    28.865839
## HLX         7.166934      8.065071      4.320037      5.190617    12.327818
## CP          4.392075      3.008328      6.152549      2.868452    26.953178
## 8138 more rows ...
## 
## $samples
##                   group lib.size norm.factors
## AI007_P45_POST   post.s 630376.5    1.0169600
## AI007_P42_POST   post.s 722098.9    0.9067228
## AI007_P41_POST   post.s 584779.2    1.1334031
## AI007_P44_POST   post.s 602080.1    1.0935932
## AI007_P40_POST   post.s 586537.3    1.1225127
## 55 more rows ...
design<- model.matrix(~0+group)
colnames(design) <- levels(group)
design
##      post.s   pre.s
## 1         1       0
## 2         1       0
## 3         1       0
## 4         1       0
## 5         1       0
## 6         1       0
## 7         1       0
## 8         1       0
## 9         1       0
## 10        1       0
## 11        1       0
## 12        1       0
## 13        1       0
## 14        1       0
## 15        1       0
## 16        1       0
## 17        1       0
## 18        1       0
## 19        1       0
## 20        1       0
## 21        1       0
## 22        1       0
## 23        1       0
## 24        1       0
## 25        1       0
## 26        1       0
## 27        1       0
## 28        1       0
## 29        1       0
## 30        1       0
## 31        0       1
## 32        0       1
## 33        0       1
## 34        0       1
## 35        0       1
## 36        0       1
## 37        0       1
## 38        0       1
## 39        0       1
## 40        0       1
## 41        0       1
## 42        0       1
## 43        0       1
## 44        0       1
## 45        0       1
## 46        0       1
## 47        0       1
## 48        0       1
## 49        0       1
## 50        0       1
## 51        0       1
## 52        0       1
## 53        0       1
## 54        0       1
## 55        0       1
## 56        0       1
## 57        0       1
## 58        0       1
## 59        0       1
## 60        0       1
## attr(,"assign")
## [1] 1 1
## attr(,"contrasts")
## attr(,"contrasts")$group
## [1] "contr.treatment"
par(mfrow= c(1,1))
v<- voom(y,design, plot= TRUE)

v
## An object of class "EList"
## $targets
##                   group lib.size norm.factors
## AI007_P45_POST   post.s 641067.7    1.0169600
## AI007_P42_POST   post.s 654743.6    0.9067228
## AI007_P41_POST   post.s 662790.6    1.1334031
## AI007_P44_POST   post.s 658430.7    1.0935932
## AI007_P40_POST   post.s 658395.6    1.1225127
## 55 more rows ...
## 
## $E
##        AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST
## CLASP1       3.777680       3.499812       3.995957       3.863328
## TSC2         5.028137       5.034670       4.517381       5.082024
## ERGIC2       5.273400       5.619286       5.815794       5.674836
## HLX          3.446155       3.580151       4.187925       2.875411
## CP           4.227836       5.329735       3.339148       3.289875
##        AI007_P40_POST AI007_P43_POST AI007_P62_POST AI007_P64_POST
## CLASP1       4.350648       3.779075      3.9406886       3.723906
## TSC2         5.140765       4.736085      5.1650792       5.288600
## ERGIC2       5.702849       5.692554      5.6059855       5.074903
## HLX          3.778476       2.610761      2.9175689       3.589357
## CP           2.340729       5.520465     -0.2295336       3.071719
##        AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
## CLASP1       3.920196       3.865721      3.9113302      3.8097907
## TSC2         4.845943       5.428042      5.0470436      4.7583859
## ERGIC2       5.346705       5.334955      5.5772758      5.6409552
## HLX          3.131612       3.317754      4.0348023      4.0879174
## CP           4.283932       4.686791      0.3007802     -0.3661861
##        AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST
## CLASP1       3.757951       4.247978       4.021887       3.866923
## TSC2         5.065127       4.968671       4.570225       5.052201
## ERGIC2       5.342927       5.385991       5.772782       5.940957
## HLX          3.641642       3.526324       3.536324       2.870151
## CP           3.841803       3.865861       1.973689       3.516741
##        AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST
## CLASP1       3.811409      3.8679597       3.910493       4.208907
## TSC2         4.756206      4.7737694       4.628422       4.745282
## ERGIC2       5.600084      5.6043939       5.704826       5.849329
## HLX          4.064640      3.5387165       3.033299       4.117657
## CP           3.305902     -0.1380667       3.996394       3.991523
##        AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
## CLASP1      3.591905      3.948276       3.814100       3.924495       3.546996
## TSC2        4.825545      4.949099       4.966402       4.741777       4.754381
## ERGIC2      5.333119      5.692387       5.801638       5.859367       5.975084
## HLX         3.689105      3.855316       3.829569       3.653321       3.308965
## CP          4.674532      4.049061       3.643141       3.792050       4.027984
##        AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST
## CLASP1      3.843889       4.161987       3.793757       3.726037      4.138434
## TSC2        4.521086       4.899236       4.953590       5.004765      4.920865
## ERGIC2      5.986542       4.648568       5.693266       5.884908      5.461749
## HLX         2.707247       3.891270       3.716766       3.214300      3.765205
## CP          1.532005       3.107535       4.382402       5.204532      4.064449
##        AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE
## CLASP1      4.336063      3.944319      4.230665      3.725594      3.822706
## TSC2        5.239511      5.263390      4.522562      4.527182      4.569332
## ERGIC2      5.259787      5.335148      5.563047      5.732055      5.484587
## HLX         3.674545      3.528344      3.994172      3.555722      3.522974
## CP          4.057865      4.924914      4.685596      4.784957      3.122364
##        AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE AI007_P56_PRE
## CLASP1      4.154996     3.4985153      3.988573      3.855114     3.9566894
## TSC2        5.400090     5.8566907      4.753525      5.262372     5.1115462
## ERGIC2      6.572552     4.8272698      5.806402      5.359111     5.3973142
## HLX         3.013959     4.2427654      3.515774      3.081733     3.5458175
## CP          3.770432    -0.2003216      3.139045      5.025716     0.4493907
##        AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE
## CLASP1      3.842557      4.031387      3.800341     3.4019002     4.2382349
## TSC2        4.984499      4.943759      4.926516     5.8938256     5.1288954
## ERGIC2      5.586858      5.788984      5.373790     4.4252192     5.2269783
## HLX         4.156450      3.164440      3.843646     3.0343751     2.9902480
## CP          1.899963      3.360821      4.836020     0.0410904     0.5068331
##        AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE
## CLASP1      3.811574      4.243918      4.223056      3.996602     3.883110
## TSC2        4.625465      4.927853      4.886572      4.955973     4.723142
## ERGIC2      5.728585      5.363722      5.892334      5.549817     5.581099
## HLX         3.981849      3.499867      4.375188      3.809187     2.087147
## CP          4.586048      3.168891      3.252403      4.338943     6.881127
##        AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE AI007_P17_PRE AI007_P1_PRE
## CLASP1     3.631263      4.306334      3.603371      4.172570     3.786341
## TSC2       4.725780      4.668099      5.666452      5.111947     5.086078
## ERGIC2     5.419107      5.741500      5.060053      5.363579     5.450888
## HLX        3.688276      3.876884      3.322389      2.898067     3.650425
## CP         4.341357      3.822997      3.675032      3.627793     2.547273
##        AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
## CLASP1      4.339511      4.231314      3.771631      3.568651     4.006333
## TSC2        4.552299      5.481398      4.877598      5.269735     4.979936
## ERGIC2      5.822042      5.646618      5.772191      5.294558     5.661165
## HLX         3.606824      3.738690      2.879296      3.217329     4.466302
## CP          2.958621      2.451008      3.344159      2.460829     5.564000
## 8138 more rows ...
## 
## $weights
##          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]
## [1,] 6.132821 6.323556 6.437323 6.375542 6.375045 6.679664 5.206287 5.409930
## [2,] 9.072863 9.087302 9.095672 9.091149 9.091112 9.112929 9.015002 9.028571
## [3,] 9.434963 9.447456 9.452282 9.450240 9.450224 9.460068 9.380118 9.394638
## [4,] 3.547225 3.740831 3.858917 3.794548 3.794033 4.103236 2.834106 2.991010
## [5,] 2.382388 2.508922 2.585942 2.543968 2.543632 2.754007 1.926546 2.023283
##          [,9]    [,10]    [,11]    [,12]    [,13]    [,14]    [,15]    [,16]
## [1,] 6.138296 6.111870 5.134229 6.179959 6.896016 5.646705 5.731130 6.562018
## [2,] 9.073285 9.071275 9.010048 9.076480 9.127719 9.043595 9.048770 9.104646
## [3,] 9.435328 9.433563 9.374337 9.438093 9.466732 9.408336 9.413053 9.456332
## [4,] 3.552707 3.526290 2.779316 3.594566 4.303067 3.173760 3.236299 3.990597
## [5,] 2.385979 2.368675 1.893061 2.413390 2.908688 2.137363 2.178452 2.671736
##         [,17]    [,18]    [,19]    [,20]    [,21]    [,22]    [,23]    [,24]
## [1,] 5.765628 5.587190 6.647784 6.033025 2.632132 5.639361 7.039087 5.400551
## [2,] 9.050859 9.039891 9.110701 9.066553 8.486099 9.043141 9.137201 9.027959
## [3,] 9.414957 9.404959 9.459063 9.429259 9.144571 9.407922 9.471000 9.394081
## [4,] 3.261958 3.129894 4.074121 3.462902 1.468931 3.168337 4.437364 2.983717
## [5,] 2.195304 2.108527 2.731585 2.327137 1.089671 2.133799 3.013405 2.018800
##         [,25]    [,26]    [,27]    [,28]    [,29]    [,30]    [,31]    [,32]
## [1,] 5.153176 6.248899 6.491184 5.940153 6.022378 6.363891 6.570632 7.157016
## [2,] 9.011358 9.081713 9.099573 9.061198 9.065944 9.090290 9.136594 9.186961
## [3,] 9.375867 9.442620 9.454043 9.424380 9.428705 9.449852 9.400262 9.436130
## [4,] 2.793686 3.664402 3.915504 3.392700 3.454831 3.782474 3.696647 4.276691
## [5,] 1.901630 2.459028 2.622823 2.281107 2.321847 2.536092 2.841339 3.312300
##         [,33]    [,34]    [,35]    [,36]    [,37]    [,38]    [,39]    [,40]
## [1,] 6.923006 7.233127 6.308359 5.046473 5.408590 6.096481 6.424026 5.601566
## [2,] 9.165332 9.195512 9.117424 9.033454 9.057927 9.101248 9.125993 9.070284
## [3,] 9.421066 9.442083 9.382198 9.283779 9.316388 9.364521 9.391210 9.330600
## [4,] 4.042820 4.373608 3.447620 2.514255 2.763415 3.253148 3.556333 2.900592
## [5,] 3.111432 3.395501 2.648695 1.956048 2.137802 2.498335 2.732780 2.237336
##         [,41]    [,42]    [,43]    [,44]    [,45]    [,46]    [,47]    [,48]
## [1,] 6.755853 6.739950 5.646449 3.737042 5.764979 6.830537 6.463298 5.488770
## [2,] 9.151407 9.150061 9.073149 8.915485 9.080804 9.157678 9.128860 9.063125
## [3,] 9.411359 9.410421 9.333821 9.172815 9.342184 9.415731 9.393658 9.322365
## [4,] 3.877982 3.862234 2.932826 1.850097 3.018544 3.952390 3.593641 2.820133
## [5,] 2.981687 2.969496 2.260671 1.480039 2.322633 3.039293 2.761642 2.179000
##         [,49]    [,50]    [,51]    [,52]    [,53]    [,54]    [,55]    [,56]
## [1,] 6.507533 6.946668 6.234744 5.558846 5.142351 6.667052 7.060982 6.337697
## [2,] 9.132066 9.167271 9.111874 9.067593 9.039981 9.143844 9.176533 9.119615
## [3,] 9.396396 9.422417 9.376132 9.327504 9.292538 9.406085 9.428869 9.384592
## [4,] 3.635909 4.063154 3.379340 2.870027 2.577944 3.790476 4.161968 3.475028
## [5,] 2.794343 3.129874 2.595895 2.215190 2.002630 2.913953 3.214137 2.669892
##         [,57]    [,58]    [,59]    [,60]
## [1,] 6.519827 6.722476 6.080606 5.509847
## [2,] 9.132952 9.148578 9.100300 9.064476
## [3,] 9.397153 9.409387 9.363485 9.323919
## [4,] 3.647702 3.844969 3.242165 2.835108
## [5,] 2.803467 2.956131 2.489845 2.189867
## 8138 more rows ...
## 
## $design
##     post.s   pre.s
## 1        1       0
## 2        1       0
## 3        1       0
## 4        1       0
## 5        1       0
## 55 more rows ...
fit<- lmFit(v)
names(fit)
##  [1] "coefficients"     "stdev.unscaled"   "sigma"            "df.residual"     
##  [5] "cov.coefficients" "pivot"            "rank"             "Amean"           
##  [9] "method"           "design"

Coding error is still being resolved

#cont.matrix<- makeContrasts(PRE.svPOST.s= pre.s - post.s, levels= design)

Almost to volcano plot figure however, some coding issues are still being resolved

Multiple sequence analysis and Pathway analysis

ESR1SequenceFile<- system.file("/Users/heatherotto/Downloads/ESR1_refseq_transcript-2.fasta")
ESR1Sequences<- readAAStringSet("/Users/heatherotto/Downloads/ESR1_refseq_transcript-2.fasta")
ESR1Sequences
## AAStringSet object of length 3:
##     width seq                                               names               
## [1]  6327 AGCTGGCGGAGGGCGTTCGTCCT...TTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
## [2]  7949 TGTACATTTATATTTTCTAATGA...TTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
## [3]  2438 GTATTTTTCAGAATATCCTTTCT...AGGGTTTCCCCGCCACAGTCTGA XM_015137107.2 PR...
FirstAlignment<- msa(ESR1Sequences)
## use default substitution matrix
FirstAlignment
## CLUSTAL 2.1  
## 
## Call:
##    msa(ESR1Sequences)
## 
## MsaAAMultipleAlignment with 3 rows and 8024 columns
##     aln                                                    names
## [1] --------------------------...TGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
## [2] TGTACATTTATATTTTCTAATGAAAA...TGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
## [3] --------------------------...------------------------- XM_015137107.2 PR...
## Con --------------------------...TGTTCAAATAAAGAATTAAACTAAA Consensus
print(FirstAlignment,  show= "complete")
## 
## MsaAAMultipleAlignment with 3 rows and 8024 columns
##     aln (1..54)                                            names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTATAACCTTCAGTTCAGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (55..108)                                          names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ATTCATTAGCTGTCCTATTTTGAGAACTGTTGCTCTATGTAATTTTCGTCTCTG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (109..162)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TATTGATGTGTAAAACTGGTTTTAACAGGTAGCTAAATGCTGTTTGAAAAGCAT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (163..216)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ACTTCACCCATTCTGGCAACTAAAATAATTGAAAGATTTAATTAATTTAGAAAA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (217..270)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] AATATTTCACTTTCAAAACACTTAAACTGTTCAGAGCATGTTATTCAATAATCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (271..324)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ACCTTTCACCAGAAATCATAATAAACACAATAAAAATGCTTACAGAACCCCCAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (325..378)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] AATGCGTTAGTATACACGATTATTCCTTGTGTAAGTGAATCTTGTTGAGATTTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (379..432)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ATGTTCAGTCAATTGAAATTAAATACTTTACATATTAACTAAAATGTGTCCTGC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (433..486)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TCTATGTATTCTGGAGAAGTTACTCTCAGACAAATTTACATATTTAAATTATTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (487..540)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TATGGGCTAACTGATAAGTATAGAGAAGACTGAAGACAGTTAAGATCATTTATT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (541..594)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TCAAAATGTTTTAAAGTGTTGATTATTTATTTTGGTTTTCTTTCTTTCCCATGC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (595..648)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] CAGTTTTGAGATGCACCTCTTACTTGGCAGCTGTTCCTCTGTACTGGGTACTGG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (649..702)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] GACAGAGAGAAATACAGTAGCAAGAGGGAGATCCTGCCTCCGCCCCATTCTACC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (703..756)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ATTCTCACTGCCAGAAAGCCAGCCTTTTTTCAAGGCTTGTAGAGAAGAAAATGC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (757..810)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] GAAAATATTTTTAAAAACTCATTTAAAGTACCTACTGCATAAACCACACCAGAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (811..864)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ATGATGAGATATTAAAATGTCAATATTATTAAAAATTTTTAATATGATTTTACA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (865..918)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] GCCCCTTTGCTACTTTAAAATGTTTATCTTAGTGTTAAACAAACAATCAATAAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (919..972)                                         names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] CTCATAAACTTAAAAATTGCTGCAGGAAATACCGGACAGTTTATGGAAGGATCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (973..1026)                                        names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TATGACAGAAGGAAGGGCTGAAGAGTGTGAGAAGCTAGACCTCTGCAGGTTACC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (1027..1080)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] GAAGTCAAGAACCTCATTAATCAGTAACAAGAAGTGCAGAGCGGGCTTTTGAGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (1081..1134)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] CCATGCCTGAGTAAGAAAGTCCCAAAAAACACTCACAGAAGATATTTCCTTGCC XM_009452243.3 PR...
## [3] --------------------------------------------GTATTTTTCA XM_015137107.2 PR...
## Con --------------------------------------------?T???TT?C? Consensus 
## 
##     aln (1135..1188)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] CCTGCTTTTAGTTTAGCTGTAGCTAACTTTGGATTAACAAAATTTATGTGCTGA XM_009452243.3 PR...
## [3] GAATATCCTTTCTAGGTACAGTTTTTCAGTTCTAGTGCACAGAATGGAAACTTG XM_015137107.2 PR...
## Con ?????T??T???T??G???????T??C??T???????CA?A???T?????CT?? Consensus 
## 
##     aln (1189..1242)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] ATGATGTTTTATTTTTTTTTCCAACTCCACATGCCTGTCTAGACTTCAAGCTTT XM_009452243.3 PR...
## [3] TTACCTGCTATACCACATTTTCACTAGGATGTGATGTATTTATCACAAACAACA XM_015137107.2 PR...
## Con ?T??????T????????TTT?CA?????A??TG??????T???C???AA????? Consensus 
## 
##     aln (1243..1296)                                       names
## [1] ---------------------AGCTG---------------------------- NM_000125.4 Homo ...
## [2] ATTATGAATAAAGAGAAAATCGGCTGGATGGCATAAAAAATATTTCAGGCAGAT XM_009452243.3 PR...
## [3] GTATTGGTCAACATTTTCCCTCGCTGTGAAGTGCACATTTGACATCCTTTAGAA XM_015137107.2 PR...
## Con ?T??TG???AA???????????GCTG????G???A?A????A??TC????AGA? Consensus 
## 
##     aln (1297..1350)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TAACACATGATT--------------------TACCTCTTCTTGAACATCCATC XM_009452243.3 PR...
## [3] AAATTACTGACGGTTTTGAGACGATTGTTTTGTGCTTTCTTTCAGTCAACGTAA XM_015137107.2 PR...
## Con ?AA????TGA??--------------------T?C?T??T?T????CA?C???? Consensus 
## 
##     aln (1351..1404)                                       names
## [1] -----------GCGGAGGGCGTTCGTCCTGG------------GACTG------ NM_000125.4 Homo ...
## [2] TTAATGGAAGTGCTAAGAAAGTTAGATTCGG------------GCCTGGCTTGG XM_009452243.3 PR...
## [3] TTTTCCCGAAAGCAGAGATGACTCTTCCAGACATGCTAACAATGCCTG-----A XM_015137107.2 PR...
## Con TT??????A??GC?GAGA??GTTCGTCC?GG------------GCCTG-----? Consensus 
## 
##     aln (1405..1458)                                       names
## [1] ------------CACTTGCTCC-------------------------------- NM_000125.4 Homo ...
## [2] CAAAAGCAAGGCCACCCCCTCCTCTATTTTTTCAATGAGATTTTCCAATCCTAG XM_009452243.3 PR...
## [3] ACAAACTGTGTAAGCTTAGTCCAAAAAAAATATTTG------------------ XM_015137107.2 PR...
## Con ??AAA????G??CACTT?CTCC???A????T?????------------------ Consensus 
## 
##     aln (1459..1512)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] TCAAATGGTGGTGCTAGTTCTTTATTTTTGAGTTACTGCATTTCCTAATTTCAT XM_009452243.3 PR...
## [3] -------------------------ATTAATAGATTTTATTTTGGTAGATTCTA XM_015137107.2 PR...
## Con -------------------------?TT????????T???TTT??TA??TTC?? Consensus 
## 
##     aln (1513..1566)                                       names
## [1] -----------CGTCGGG-------TCGCCCGGCTTC----------------- NM_000125.4 Homo ...
## [2] GGTCGTAACAGCCTCCTG-------TCTACCGACTCAGAACGGATTTTACCAAA XM_009452243.3 PR...
## [3] AGGTTCTAAGCAGTCAGAGAAATAATCGCAGAGCCTCAAATATCTCCAAAATCT XM_015137107.2 PR...
## Con ?G?????A???CGTC?GG-------TCGCCCGGCTTC?AA????T???A????? Consensus 
## 
##     aln (1567..1620)                                       names
## [1] ---ACCGGACCCGCAG--------------------GCTCCCGGGGCAGGG--- NM_000125.4 Homo ...
## [2] ---ACTGAAAATGCAG--------------------GCTCCATGCTCAGAAGCT XM_009452243.3 PR...
## [3] GATACCAATCCCTTTGATTGTGAATTATATTCTGTAGCTACCAAAGAAGGGAGA XM_015137107.2 PR...
## Con ---ACCGAACCCGCAG--------------------GCTCCC?G?GCAGGG??? Consensus 
## 
##     aln (1621..1674)                                       names
## [1] ------CCGGGGC----------CAGAG-----CTCGCGTGTCGGCGGGACATG NM_000125.4 Homo ...
## [2] CTTTAACAGGCTC----------GAAAGGTCCATGCTCCTTTCTCCTGCCCATT XM_009452243.3 PR...
## [3] AGAAAACTAGGAAGGAGTAAGCACAAAGATCTCTTCACGT-TCTCCGGAACTGT XM_015137107.2 PR...
## Con ????AAC?GGG?C----------CAAAG?TC??TTC?CGT?TCTCCGG?ACATT Consensus 
## 
##     aln (1675..1728)                                       names
## [1] CGCTG-----------------------------CGTCGCCTCTA--------- NM_000125.4 Homo ...
## [2] CTATAGCATAAGAAGACAGTCTCTGAGTGATAATCTTCTCTTCAAGAAGAAGAA XM_009452243.3 PR...
## [3] AGTAGCAAATAGCAG-----------------CACGGCGCTTCTTGAAAAAGG- XM_015137107.2 PR...
## Con CG?TG??A??AG?AG-----------------??CGTCGCTTCTAGAA?AAG?- Consensus 
## 
##     aln (1729..1782)                                       names
## [1] ------------------ACCTCGGGCTGTGCTCTTTTTCCAG----------- NM_000125.4 Homo ...
## [2] AACTAGGAAGGAGTAAGCACAAAGATCTCTTCACATTCTCTGGGACTGCGGTAC XM_009452243.3 PR...
## [3] --------------ATGTAGATTTTAATCTGAACTTTGAACCG----------- XM_015137107.2 PR...
## Con --------------A?G?ACAT?G??CTCTGCACTTT?TCC?G----------- Consensus 
## 
##     aln (1783..1836)                                       names
## [1] ------------------------------------------------------ NM_000125.4 Homo ...
## [2] CAAATATCAGCACAGCACTTCTTGAAAAAGGATGTAGATTTTAATCTGAACTTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ------------------------------------------------------ Consensus 
## 
##     aln (1837..1890)                                       names
## [1] --------------GTGGCCCGCCGGTTTCTGAGCCTTCTGCCCTGCGGGGACA NM_000125.4 Homo ...
## [2] GAACCATCACTGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACA XM_009452243.3 PR...
## [3] ------TCATTGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACA XM_015137107.2 PR...
## Con ------TCA?TGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACA Consensus 
## 
##     aln (1891..1944)                                       names
## [1] CGGTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAA NM_000125.4 Homo ...
## [2] CGGTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAA XM_009452243.3 PR...
## [3] CGGTCTGCGCCCTGCCCACGGCCACGGACCATGACCATGACCCTCCACACCAAA XM_015137107.2 PR...
## Con CGGTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAA Consensus 
## 
##     aln (1945..1998)                                       names
## [1] GCATCTGGGATGGCCCTACTGCATCAGATCCAAGGGAACGAGCTGGAGCCCCTG NM_000125.4 Homo ...
## [2] GCATCCGGGATGGCCCTACTGCATCAGATCCAAGGGAACGAGCTGGAGCCCCTG XM_009452243.3 PR...
## [3] GCATCCGGGATGGCCCTACTGCATCAGATCCAAGGGAACGAGCTGGAGCCCCTG XM_015137107.2 PR...
## Con GCATCCGGGATGGCCCTACTGCATCAGATCCAAGGGAACGAGCTGGAGCCCCTG Consensus 
## 
##     aln (1999..2052)                                       names
## [1] AACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACCTG NM_000125.4 Homo ...
## [2] AACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTG XM_009452243.3 PR...
## [3] AACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTG XM_015137107.2 PR...
## Con AACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTG Consensus 
## 
##     aln (2053..2106)                                       names
## [1] GACAGCAGCAAGCCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTC NM_000125.4 Homo ...
## [2] GACAGCAGCAAGCCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTC XM_009452243.3 PR...
## [3] GACAGCAGCAAGCCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTC XM_015137107.2 PR...
## Con GACAGCAGCAAGCCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTC Consensus 
## 
##     aln (2107..2160)                                       names
## [1] AACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGTCAGACCGGCCTCCCCTAC NM_000125.4 Homo ...
## [2] AACGCCGCGGCCGCGGCCAACGCGCAGGTCTACGGTCAGACCGGCCTCCCCTAC XM_009452243.3 PR...
## [3] AACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGCCAGACTGGCCTCCCGTAC XM_015137107.2 PR...
## Con AACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGTCAGACCGGCCTCCCCTAC Consensus 
## 
##     aln (2161..2214)                                       names
## [1] GGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCC NM_000125.4 Homo ...
## [2] GGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTCGGGGGTTTCCCC XM_009452243.3 PR...
## [3] GGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCC XM_015137107.2 PR...
## Con GGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCC Consensus 
## 
##     aln (2215..2268)                                       names
## [1] CCACTCAACAGCGTGTCTCCGAGCCCGCTGATGCTACTGCACCCGCCGCCGCAG NM_000125.4 Homo ...
## [2] CCACTCAACAGCGTGTCTCCGAGCCCGCTGATGCTACTGCACCCGCCGCCGCAG XM_009452243.3 PR...
## [3] CCACTCAACAGCGTGTCTCCGAGCCCGCTGATGCTGCTGCACCCGCCGCCGCAG XM_015137107.2 PR...
## Con CCACTCAACAGCGTGTCTCCGAGCCCGCTGATGCTACTGCACCCGCCGCCGCAG Consensus 
## 
##     aln (2269..2322)                                       names
## [1] CTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC NM_000125.4 Homo ...
## [2] CTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC XM_009452243.3 PR...
## [3] CTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC XM_015137107.2 PR...
## Con CTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC Consensus 
## 
##     aln (2323..2376)                                       names
## [1] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCA NM_000125.4 Homo ...
## [2] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCA XM_009452243.3 PR...
## [3] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCTCCGGCATTCTACAGGCCA XM_015137107.2 PR...
## Con GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCA Consensus 
## 
##     aln (2377..2430)                                       names
## [1] AATTCAGATAATCGACGCCAGGGTGGCAGAGAAAGATTGGCCAGTACCAATGAC NM_000125.4 Homo ...
## [2] AATTCAGATAATCGACGCCAGGGTGGCAGAGAAAGATTGGCCAGTACCAATGAC XM_009452243.3 PR...
## [3] AATTCAGATAATCGACGCCAGGGTGGCAGAGAGAGATTGGCCAGTACCAATGAC XM_015137107.2 PR...
## Con AATTCAGATAATCGACGCCAGGGTGGCAGAGAAAGATTGGCCAGTACCAATGAC Consensus 
## 
##     aln (2431..2484)                                       names
## [1] AAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGC NM_000125.4 Homo ...
## [2] AAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGC XM_009452243.3 PR...
## [3] AAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGC XM_015137107.2 PR...
## Con AAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGC Consensus 
## 
##     aln (2485..2538)                                       names
## [1] AATGACTATGCTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAG NM_000125.4 Homo ...
## [2] AATGACTATGCTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAG XM_009452243.3 PR...
## [3] AATGACTATGCTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAG XM_015137107.2 PR...
## Con AATGACTATGCTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAG Consensus 
## 
##     aln (2539..2592)                                       names
## [1] GCCTTCTTCAAGAGAAGTATTCAAG------GACATAACGACTATATGTGTCCA NM_000125.4 Homo ...
## [2] GCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGACTATATGTGTCCA XM_009452243.3 PR...
## [3] GCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGACTATATGTGTCCA XM_015137107.2 PR...
## Con GCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGACTATATGTGTCCA Consensus 
## 
##     aln (2593..2646)                                       names
## [1] GCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGC NM_000125.4 Homo ...
## [2] GCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGC XM_009452243.3 PR...
## [3] GCCACCAACCAGTGCACCATTGATAAGAACAGGAGGAAGAGCTGCCAGGCCTGC XM_015137107.2 PR...
## Con GCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGC Consensus 
## 
##     aln (2647..2700)                                       names
## [1] CGGCTCCGTAAATGCTACGAAGTGGGAATGATGAAAGGTGGGATACGAAAAGAC NM_000125.4 Homo ...
## [2] CGGCTCCGCAAATGCTACGAAGTGGGAATGATGAAAGGTGGGATACGAAAAGAC XM_009452243.3 PR...
## [3] CGGCTCCGCAAATGCTACGAAGTGGGAATGATGAAAGGTGGGATACGAAAAGAC XM_015137107.2 PR...
## Con CGGCTCCGCAAATGCTACGAAGTGGGAATGATGAAAGGTGGGATACGAAAAGAC Consensus 
## 
##     aln (2701..2754)                                       names
## [1] CGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGGGC NM_000125.4 Homo ...
## [2] CGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGGGC XM_009452243.3 PR...
## [3] CGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGGGC XM_015137107.2 PR...
## Con CGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGGGC Consensus 
## 
##     aln (2755..2808)                                       names
## [1] AGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGC NM_000125.4 Homo ...
## [2] AGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGC XM_009452243.3 PR...
## [3] AGGGGTGAAGTGGGGTCCGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGC XM_015137107.2 PR...
## Con AGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGC Consensus 
## 
##     aln (2809..2862)                                       names
## [1] CCGCTCATGATCAAACGCTCTAAGAAGAACAGCCTGGCCTTGTCCCTGACGGCC NM_000125.4 Homo ...
## [2] CCGCTCATGATCAAACACTCTAAGAAGAACAGCCCGGCCTTGTCCCTGACGGCC XM_009452243.3 PR...
## [3] CCGCTCATGATCAAGCACTCTAAGAAGAACAGCCCGGCCTTGTCCCTGACGGCC XM_015137107.2 PR...
## Con CCGCTCATGATCAAACACTCTAAGAAGAACAGCCCGGCCTTGTCCCTGACGGCC Consensus 
## 
##     aln (2863..2916)                                       names
## [1] GACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCCGATACTCTATTCCGAG NM_000125.4 Homo ...
## [2] GACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCCCATACTCTATTCCGAG XM_009452243.3 PR...
## [3] GACCAGATGGTCAGTGCCTTGCTGGATGCTGAGCCCCCTATACTCTATTCCGAG XM_015137107.2 PR...
## Con GACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCC?ATACTCTATTCCGAG Consensus 
## 
##     aln (2917..2970)                                       names
## [1] TATGATCCTACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAAC NM_000125.4 Homo ...
## [2] TATGATCCTACCAGACCCTTCAGTGAGGCTTCGATGATGGGCTTACTGACCAAC XM_009452243.3 PR...
## [3] TATGATCCTACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAAC XM_015137107.2 PR...
## Con TATGATCCTACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAAC Consensus 
## 
##     aln (2971..3024)                                       names
## [1] CTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCGAAGAGGGTGCCAGGC NM_000125.4 Homo ...
## [2] CTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAAAGAGGGTGCCAGGC XM_009452243.3 PR...
## [3] CTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAAAGAGGGTGCCAGGC XM_015137107.2 PR...
## Con CTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAAAGAGGGTGCCAGGC Consensus 
## 
##     aln (3025..3078)                                       names
## [1] TTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTA NM_000125.4 Homo ...
## [2] TTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTA XM_009452243.3 PR...
## [3] TTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTA XM_015137107.2 PR...
## Con TTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTA Consensus 
## 
##     aln (3079..3132)                                       names
## [1] GAGATCCTGATGATTGGTCTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTA NM_000125.4 Homo ...
## [2] GAGATCCTGATGATTGGTCTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTC XM_009452243.3 PR...
## [3] GAGATCCTGATGATTGGTCTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTC XM_015137107.2 PR...
## Con GAGATCCTGATGATTGGTCTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTC Consensus 
## 
##     aln (3133..3186)                                       names
## [1] CTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGAGGGC NM_000125.4 Homo ...
## [2] CTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGAGGGC XM_009452243.3 PR...
## [3] CTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGAGGGC XM_015137107.2 PR...
## Con CTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGAGGGC Consensus 
## 
##     aln (3187..3240)                                       names
## [1] ATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATG NM_000125.4 Homo ...
## [2] ATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATG XM_009452243.3 PR...
## [3] ATGGTGGAGATCTTCGACATGTTACTGGCCACATCATCTCGGTTCCGCATGATG XM_015137107.2 PR...
## Con ATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATG Consensus 
## 
##     aln (3241..3294)                                       names
## [1] AATCTGCAGGGAGAGGAGTTTGTGTGCCTCAAATCTATTATTTTGCTTAATTCT NM_000125.4 Homo ...
## [2] AATCTGCAGGGAGAGGAGTTTGTGTGCCTCAAGTCTATTATTTTGCTTAATTCT XM_009452243.3 PR...
## [3] AATCTGCAGGGAGAGGAGTTTGTGTGCCTCAAATCTATTATTTTGCTTAATTCT XM_015137107.2 PR...
## Con AATCTGCAGGGAGAGGAGTTTGTGTGCCTCAAATCTATTATTTTGCTTAATTCT Consensus 
## 
##     aln (3295..3348)                                       names
## [1] GGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCAT NM_000125.4 Homo ...
## [2] GGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCAT XM_009452243.3 PR...
## [3] GGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCAT XM_015137107.2 PR...
## Con GGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCAT Consensus 
## 
##     aln (3349..3402)                                       names
## [1] ATCCACCGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAG NM_000125.4 Homo ...
## [2] ATCCACCGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAG XM_009452243.3 PR...
## [3] ATCCACCGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAG XM_015137107.2 PR...
## Con ATCCACCGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAG Consensus 
## 
##     aln (3403..3456)                                       names
## [1] GCAGGCCTGACCCTGCAGCAGCAGCACCAGCGGCTGGCCCAGCTCCTCCTCATC NM_000125.4 Homo ...
## [2] GCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGCCCAGCTCCTCCTCATC XM_009452243.3 PR...
## [3] GCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGCCCAGCTCCTCCTCATC XM_015137107.2 PR...
## Con GCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGCCCAGCTCCTCCTCATC Consensus 
## 
##     aln (3457..3510)                                       names
## [1] CTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATG NM_000125.4 Homo ...
## [2] CTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATG XM_009452243.3 PR...
## [3] CTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATG XM_015137107.2 PR...
## Con CTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATG Consensus 
## 
##     aln (3511..3564)                                       names
## [1] AAGTGCAAGAACGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCC NM_000125.4 Homo ...
## [2] AAGTGCAAGAACGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCC XM_009452243.3 PR...
## [3] AAGTGCAAGAATGTGGTGCCCCTCTACGACCTGCTGCTGGAGATGCTGGACGCC XM_015137107.2 PR...
## Con AAGTGCAAGAACGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCC Consensus 
## 
##     aln (3565..3618)                                       names
## [1] CACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCATCCGTGGAGGAGACGGAC NM_000125.4 Homo ...
## [2] CACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCGTGGAGGAGACGGAC XM_009452243.3 PR...
## [3] CACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCATGGAGGAGACGGAC XM_015137107.2 PR...
## Con CACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCGTGGAGGAGACGGAC Consensus 
## 
##     aln (3619..3672)                                       names
## [1] CAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTAT NM_000125.4 Homo ...
## [2] CAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTAT XM_009452243.3 PR...
## [3] CAAAGCCACTTGGCCACCGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTAT XM_015137107.2 PR...
## Con CAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTAT Consensus 
## 
##     aln (3673..3726)                                       names
## [1] TACATCACGGGGGAGGCAGAGGGTTTCCCTGCCACGGTCTGAGAGCTCCCTGGC NM_000125.4 Homo ...
## [2] TACATCACGGGGGAGGCAGAGGGTTTCCCTGCCACAGTCTGAGAGTTCCCTGGC XM_009452243.3 PR...
## [3] TACATCACGGGGGACGCAGAGGGTTTCCCCGCCACAGTCTGA------------ XM_015137107.2 PR...
## Con TACATCACGGGGGAGGCAGAGGGTTTCCCTGCCACAGTCTGAGAG?TCCCTGGC Consensus 
## 
##     aln (3727..3780)                                       names
## [1] TCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTT NM_000125.4 Homo ...
## [2] TCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTT Consensus 
## 
##     aln (3781..3834)                                       names
## [1] TAGCCAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCT NM_000125.4 Homo ...
## [2] TAGCCAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TAGCCAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCT Consensus 
## 
##     aln (3835..3888)                                       names
## [1] TTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTTCTTAGTGGCACATCTTCT NM_000125.4 Homo ...
## [2] TTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTTCTTAGTGGCACATCTTCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTTCTTAGTGGCACATCTTCT Consensus 
## 
##     aln (3889..3942)                                       names
## [1] GTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCT NM_000125.4 Homo ...
## [2] GTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCT Consensus 
## 
##     aln (3943..3996)                                       names
## [1] CTCTTTCCCCCTTGCTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAG NM_000125.4 Homo ...
## [2] CTCTTTCCCCCTTGCTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CTCTTTCCCCCTTGCTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAG Consensus 
## 
##     aln (3997..4050)                                       names
## [1] CTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTAAGCTACTT NM_000125.4 Homo ...
## [2] CTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTAAGCTACTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTAAGCTACTT Consensus 
## 
##     aln (4051..4104)                                       names
## [1] GTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAA NM_000125.4 Homo ...
## [2] GTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAA Consensus 
## 
##     aln (4105..4158)                                       names
## [1] ATGGCTCTAAGAATAAGCCACAGCAAAGAATTTAAAGTGGCTCCTTTAATTGGT NM_000125.4 Homo ...
## [2] ATGGCTCTAAGAATAAGCCACAGCAAAGAATTTAAAGTGGCTCCTTTAATTGGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ATGGCTCTAAGAATAAGCCACAGCAAAGAATTTAAAGTGGCTCCTTTAATTGGT Consensus 
## 
##     aln (4159..4212)                                       names
## [1] GACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTAT NM_000125.4 Homo ...
## [2] GACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTAT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTAT Consensus 
## 
##     aln (4213..4266)                                       names
## [1] GGCAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTA NM_000125.4 Homo ...
## [2] GGCAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GGCAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTA Consensus 
## 
##     aln (4267..4320)                                       names
## [1] GCAGAGTATCTGGTGATTGTCAATTCATTCCCCCTATAGGAATACAAGGGGCAC NM_000125.4 Homo ...
## [2] GCAGAGTATCTGGTGATTGTCAATTCATTCCCCCTATAGGAATACAAGGGGCAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GCAGAGTATCTGGTGATTGTCAATTCATTCCCCCTATAGGAATACAAGGGGCAC Consensus 
## 
##     aln (4321..4374)                                       names
## [1] ACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCA NM_000125.4 Homo ...
## [2] ACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCA Consensus 
## 
##     aln (4375..4428)                                       names
## [1] GATTCAGATGTGCTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTT NM_000125.4 Homo ...
## [2] GCTTCAGATGTGCTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con G?TTCAGATGTGCTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTT Consensus 
## 
##     aln (4429..4482)                                       names
## [1] AATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCTTAGTTAAGTC NM_000125.4 Homo ...
## [2] AATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCTTAGTTAAGTC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCTTAGTTAAGTC Consensus 
## 
##     aln (4483..4536)                                       names
## [1] TCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAA NM_000125.4 Homo ...
## [2] TCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAA Consensus 
## 
##     aln (4537..4590)                                       names
## [1] GAAAGCCCTCCCTCCCTGAACTTGCAGTAAGGTCAGCTTCAGGACCTGTTCCAG NM_000125.4 Homo ...
## [2] GAAAGCCCTCCCTCCCTGAACTTGCAGTAAGGTCAGCTTCAGGACCTGTTCCAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GAAAGCCCTCCCTCCCTGAACTTGCAGTAAGGTCAGCTTCAGGACCTGTTCCAG Consensus 
## 
##     aln (4591..4644)                                       names
## [1] TGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC NM_000125.4 Homo ...
## [2] TGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC Consensus 
## 
##     aln (4645..4698)                                       names
## [1] TGTTCACTGTGGTGATGCATGATGAGGGTAAATGGTAGTTGAAAGGAGCAGGGG NM_000125.4 Homo ...
## [2] TGTTCACTGTGGTGATGCATGATGAGAGTAAATGGTAGTTGAAAGGAGCAGGGG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TGTTCACTGTGGTGATGCATGATGAG?GTAAATGGTAGTTGAAAGGAGCAGGGG Consensus 
## 
##     aln (4699..4752)                                       names
## [1] CCCTGGTGTTGCATTTAGCCCTGGGGCATGGAGCTGAACAGTACTTGTGCAGGA NM_000125.4 Homo ...
## [2] CCCTGGTGTTGCATTGAGCCCTGGGGCATGGAGCTGAACAGTACTTGTGCAGGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CCCTGGTGTTGCATT?AGCCCTGGGGCATGGAGCTGAACAGTACTTGTGCAGGA Consensus 
## 
##     aln (4753..4806)                                       names
## [1] TTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGT NM_000125.4 Homo ...
## [2] TTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGT Consensus 
## 
##     aln (4807..4860)                                       names
## [1] TCTGAGGCACAGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACC NM_000125.4 Homo ...
## [2] TCTGAGGCACAGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCTGAGGCACAGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACC Consensus 
## 
##     aln (4861..4914)                                       names
## [1] TAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTGCCCTGGGATCCC NM_000125.4 Homo ...
## [2] TAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTGCCCTGGGATCCC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTGCCCTGGGATCCC Consensus 
## 
##     aln (4915..4968)                                       names
## [1] TGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCA NM_000125.4 Homo ...
## [2] TGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCA Consensus 
## 
##     aln (4969..5022)                                       names
## [1] GCTGTCACAGCTGCTGTAGACAGCTGTGTTCCTACAATTGGCCCAGCACCCTGG NM_000125.4 Homo ...
## [2] GCTGTCACAGCTGCTGTAGACAGCTGTGTTCCTACAATTGGCCCAGCACCCTGG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GCTGTCACAGCTGCTGTAGACAGCTGTGTTCCTACAATTGGCCCAGCACCCTGG Consensus 
## 
##     aln (5023..5076)                                       names
## [1] GGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGGCC NM_000125.4 Homo ...
## [2] GGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGGCC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGGCC Consensus 
## 
##     aln (5077..5130)                                       names
## [1] TGGTCAGATTACGTATGCCCTTGGTGGTTTAGAGATAATCCAAAATCAGGGTTT NM_000125.4 Homo ...
## [2] TGGTCAGATTACCTATGCCCTTGGTGGTTTAGAGCTAATCCAAAATCAGGGTTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TGGTCAGATTAC?TATGCCCTTGGTGGTTTAGAG?TAATCCAAAATCAGGGTTT Consensus 
## 
##     aln (5131..5184)                                       names
## [1] GGTTTGGGGAAGAAAATCCTCCCCCTTCCTCCCCCGCCCCGTTCCCTACCGCCT NM_000125.4 Homo ...
## [2] GGTTTGGGGAAGAAAATCCTCCCCCTTCCTCCCCCGCCCCGTTCCCTACCGCCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GGTTTGGGGAAGAAAATCCTCCCCCTTCCTCCCCCGCCCCGTTCCCTACCGCCT Consensus 
## 
##     aln (5185..5238)                                       names
## [1] CCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAG NM_000125.4 Homo ...
## [2] CCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAG Consensus 
## 
##     aln (5239..5292)                                       names
## [1] AAAGGCTCATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCA NM_000125.4 Homo ...
## [2] AAAGGCTCATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AAAGGCTCATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCA Consensus 
## 
##     aln (5293..5346)                                       names
## [1] CAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATGTTTGATTTCCTCTG NM_000125.4 Homo ...
## [2] CAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATGTTTGATTTCCTCTG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATGTTTGATTTCCTCTG Consensus 
## 
##     aln (5347..5400)                                       names
## [1] GGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAG NM_000125.4 Homo ...
## [2] GGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAG Consensus 
## 
##     aln (5401..5454)                                       names
## [1] CCAATGACCCAGGTGAGCTGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAA NM_000125.4 Homo ...
## [2] CCAATGACCCAGGTGAGCTGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CCAATGACCCAGGTGAGCTGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAA Consensus 
## 
##     aln (5455..5508)                                       names
## [1] GTGGATTTCATTCATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACTGAGA NM_000125.4 Homo ...
## [2] GGGGATTTCATTAATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACTGAGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con G?GGATTTCATT?ATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACTGAGA Consensus 
## 
##     aln (5509..5562)                                       names
## [1] ATCTGGGAGGGCAAAAAAAAAAAAAAAGTTTTTATGTGCACTTAAATTTGGGGA NM_000125.4 Homo ...
## [2] ATCTGGGAGGGCAAAAAAAAAAAAAAG-TTTTTATGTGCACTTAAATTTGGGGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ATCTGGGAGGGCAAAAAAAAAAAAAA?-TTTTTATGTGCACTTAAATTTGGGGA Consensus 
## 
##     aln (5563..5616)                                       names
## [1] CAATTTTATGTATCTGTGTTAAGGATATGTTTAAGAACATAATTCTTTTGTTGC NM_000125.4 Homo ...
## [2] CAATTTTATGTATCTGTGTTAAGGATATGTTTAAGAACATAATTCTTTTGTTGC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CAATTTTATGTATCTGTGTTAAGGATATGTTTAAGAACATAATTCTTTTGTTGC Consensus 
## 
##     aln (5617..5670)                                       names
## [1] TGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAAT NM_000125.4 Homo ...
## [2] TGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAAT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAAT Consensus 
## 
##     aln (5671..5724)                                       names
## [1] ATATATTTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAAT NM_000125.4 Homo ...
## [2] ATATATTTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAAT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ATATATTTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAAT Consensus 
## 
##     aln (5725..5778)                                       names
## [1] TCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAAAACCAAGGAAAAATAT NM_000125.4 Homo ...
## [2] TCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAAAACCAAGGAAAAATAT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAAAACCAAGGAAAAATAT Consensus 
## 
##     aln (5779..5832)                                       names
## [1] TTAGTTTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACA NM_000125.4 Homo ...
## [2] TTAG-TTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTAG-TTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACA Consensus 
## 
##     aln (5833..5886)                                       names
## [1] GTCATTTATGCCTAAAGCCTGGTGATTATTCATTTAAATGAAGATCACATTTCA NM_000125.4 Homo ...
## [2] GTCATTTATGCCTAAAGCCTGGTGATTATTCATTTAAATGAAGATCACATTTCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GTCATTTATGCCTAAAGCCTGGTGATTATTCATTTAAATGAAGATCACATTTCA Consensus 
## 
##     aln (5887..5940)                                       names
## [1] TATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGCCTATTG NM_000125.4 Homo ...
## [2] TATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGCCTATTG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGCCTATTG Consensus 
## 
##     aln (5941..5994)                                       names
## [1] TTGGATACTGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGA NM_000125.4 Homo ...
## [2] TTGGATATTGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTGGATA?TGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGA Consensus 
## 
##     aln (5995..6048)                                       names
## [1] AAATTATTCAGGGCAGCTAATTTTGCTTTTACCAAAATATCAGTAGTAATATTT NM_000125.4 Homo ...
## [2] AAATTATTCAGGGCAGCTAATTTTGCTTTTACCAAAATATCAGTAGTAATATTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AAATTATTCAGGGCAGCTAATTTTGCTTTTACCAAAATATCAGTAGTAATATTT Consensus 
## 
##     aln (6049..6102)                                       names
## [1] TTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTT NM_000125.4 Homo ...
## [2] TTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTT Consensus 
## 
##     aln (6103..6156)                                       names
## [1] TCTTTTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGT NM_000125.4 Homo ...
## [2] TCTTTTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCTTTTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGT Consensus 
## 
##     aln (6157..6210)                                       names
## [1] AATACCAGCTAAAGCCAAACAATTATACAGTGGAAGGTTTTACATTATTCATCC NM_000125.4 Homo ...
## [2] AATACCAGCTAAAGCCAAACAATTATACAGTGGAAGGTTTTACATTATTCATCC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AATACCAGCTAAAGCCAAACAATTATACAGTGGAAGGTTTTACATTATTCATCC Consensus 
## 
##     aln (6211..6264)                                       names
## [1] AATGTGTTTCTATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACA NM_000125.4 Homo ...
## [2] AATGTGTTTGTATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AATGTGTTT?TATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACA Consensus 
## 
##     aln (6265..6318)                                       names
## [1] TCAGATGATTGAAATGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTT NM_000125.4 Homo ...
## [2] TCAGATGATTGAAATGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCAGATGATTGAAATGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTT Consensus 
## 
##     aln (6319..6372)                                       names
## [1] GTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGGCTGATGTT NM_000125.4 Homo ...
## [2] GTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGGCTGATGTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGGCTGATGTT Consensus 
## 
##     aln (6373..6426)                                       names
## [1] GGTATTGGGTGTAGGAACATGATTTAAAAAAAAACTCTTGCCTCTGCTTTCCCC NM_000125.4 Homo ...
## [2] GGTATTGGGTGTAGGAACATGATT-AAAAAAAAACTCTTGCCTCTGCTTTCCCC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GGTATTGGGTGTAGGAACATGATT-AAAAAAAAACTCTTGCCTCTGCTTTCCCC Consensus 
## 
##     aln (6427..6480)                                       names
## [1] CACTCTGAGGCAAGTTAAAATGTAAAAGATGTGATTTATCTGGGGGGCTCAGGT NM_000125.4 Homo ...
## [2] CACTCTGAGGCAAGTTAAAATTTAAAAGATGTGATTTATCTGGGGGGCTCAGGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CACTCTGAGGCAAGTTAAAAT?TAAAAGATGTGATTTATCTGGGGGGCTCAGGT Consensus 
## 
##     aln (6481..6534)                                       names
## [1] ATGGTGGGGAAGTGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAG NM_000125.4 Homo ...
## [2] ATGGTGGGGAAATGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ATGGTGGGGAA?TGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAG Consensus 
## 
##     aln (6535..6588)                                       names
## [1] TATTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAG NM_000125.4 Homo ...
## [2] TATTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TATTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAG Consensus 
## 
##     aln (6589..6642)                                       names
## [1] TAGAGTCCACTTCTGCCCTGGAGACCACAAATCAACTAGCTCCATTTACAGCCA NM_000125.4 Homo ...
## [2] TAGAGTCCACTTCTGCCCTGGAGACCACAAATCAACTAGCTGCATTTACAGCCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TAGAGTCCACTTCTGCCCTGGAGACCACAAATCAACTAGCT?CATTTACAGCCA Consensus 
## 
##     aln (6643..6696)                                       names
## [1] TTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAA NM_000125.4 Homo ...
## [2] TTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAA Consensus 
## 
##     aln (6697..6750)                                       names
## [1] GTCCATG--GAATAGCTAGTGGTCTGTGTTTCTTTTCGCCATTGCCTAGCTTGC NM_000125.4 Homo ...
## [2] GTCCATGGAGAATAGCTAGTGGTCTGTATTTCTTTTCGCCATTGCCTAGCTTGC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con GTCCATG--GAATAGCTAGTGGTCTGT?TTTCTTTTCGCCATTGCCTAGCTTGC Consensus 
## 
##     aln (6751..6804)                                       names
## [1] CGTAATGATTCTATAATGCCATCATGCAGCAATTATGAGAGGCTAGGTCATCCA NM_000125.4 Homo ...
## [2] CGTAATGATTCTGTAATGCCATCATGCAGCAATTATGAGAGGCTAGGTCATCCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CGTAATGATTCT?TAATGCCATCATGCAGCAATTATGAGAGGCTAGGTCATCCA Consensus 
## 
##     aln (6805..6858)                                       names
## [1] AAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAG NM_000125.4 Homo ...
## [2] AAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAG Consensus 
## 
##     aln (6859..6912)                                       names
## [1] TCTTTGATTTGATTTCCCTAGTAACCTTGCAGATATGTTTAACCAAGCCATAGC NM_000125.4 Homo ...
## [2] TCTTTGATTTGATTTCCCTAGTAACCTTGCAGATATGTTTAACCACGCCATAGC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCTTTGATTTGATTTCCCTAGTAACCTTGCAGATATGTTTAACCA?GCCATAGC Consensus 
## 
##     aln (6913..6966)                                       names
## [1] CCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA NM_000125.4 Homo ...
## [2] CCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA Consensus 
## 
##     aln (6967..7020)                                       names
## [1] TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATT NM_000125.4 Homo ...
## [2] TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATT Consensus 
## 
##     aln (7021..7074)                                       names
## [1] TAGGCCACTGGCTTAGAGTACTCCTTCCCCTGCATGACACTGATTACAAATACT NM_000125.4 Homo ...
## [2] TAGGCCATTGGCTTAGAGTACTCCTTCCCCTGCATGACACTGATTACAAATCCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TAGGCCA?TGGCTTAGAGTACTCCTTCCCCTGCATGACACTGATTACAAAT?CT Consensus 
## 
##     aln (7075..7128)                                       names
## [1] TTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGAGTGATCA NM_000125.4 Homo ...
## [2] TTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGAATGATCA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGA?TGATCA Consensus 
## 
##     aln (7129..7182)                                       names
## [1] CTAACACCATAGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAG NM_000125.4 Homo ...
## [2] CTAACACCATAGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CTAACACCATAGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAG Consensus 
## 
##     aln (7183..7236)                                       names
## [1] TTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGCAACCATAATTCT NM_000125.4 Homo ...
## [2] TTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGCAACCATAATTCT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGCAACCATAATTCT Consensus 
## 
##     aln (7237..7290)                                       names
## [1] CTTTGGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGT NM_000125.4 Homo ...
## [2] CTTCGGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CTT?GGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGT Consensus 
## 
##     aln (7291..7344)                                       names
## [1] TAATCCCCTGAAAACTTACTCTCAACTGGAGCAAATGAACTTTGGTCCCAAATA NM_000125.4 Homo ...
## [2] TAATCCCCTGAAAACTTACTCTCAACTGGAGCAAATGAACTTTGGTCCCAAATA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TAATCCCCTGAAAACTTACTCTCAACTGGAGCAAATGAACTTTGGTCCCAAATA Consensus 
## 
##     aln (7345..7398)                                       names
## [1] TCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTTCC NM_000125.4 Homo ...
## [2] TCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTTCC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTTCC Consensus 
## 
##     aln (7399..7452)                                       names
## [1] AATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTA NM_000125.4 Homo ...
## [2] AATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTA Consensus 
## 
##     aln (7453..7506)                                       names
## [1] ATTGCTGCCTCTATTATGGCACTTCAATTTTGCACTGTCTTTTGAGATTCAAGA NM_000125.4 Homo ...
## [2] ATTGCTGCCTCTATTATGGCACTTCAATTTTGCACTGTCTTTTGAGATTCAAGA XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con ATTGCTGCCTCTATTATGGCACTTCAATTTTGCACTGTCTTTTGAGATTCAAGA Consensus 
## 
##     aln (7507..7560)                                       names
## [1] AAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGT NM_000125.4 Homo ...
## [2] AAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGT Consensus 
## 
##     aln (7561..7614)                                       names
## [1] AAATGCTGCCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCAC NM_000125.4 Homo ...
## [2] AAATGCTGCCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con AAATGCTGCCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCAC Consensus 
## 
##     aln (7615..7668)                                       names
## [1] CCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGACACAGACCCCTTTG NM_000125.4 Homo ...
## [2] CCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGACACAGACCCCTTTG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGACACAGACCCCTTTG Consensus 
## 
##     aln (7669..7722)                                       names
## [1] CATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATG NM_000125.4 Homo ...
## [2] CATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATG XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATG Consensus 
## 
##     aln (7723..7776)                                       names
## [1] CCAGTTTCTGTTCTCTCACAGGTGATAAACAATGCTTTTTGTGCACTACATACT NM_000125.4 Homo ...
## [2] CCAGTTTCTGTTCTCTCACAGGTGATAAACAATGCTTTTTGTGCACTACATACT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CCAGTTTCTGTTCTCTCACAGGTGATAAACAATGCTTTTTGTGCACTACATACT Consensus 
## 
##     aln (7777..7830)                                       names
## [1] CTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAATTGTGTT NM_000125.4 Homo ...
## [2] CTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAATCGTGTT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con CTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAAT?GTGTT Consensus 
## 
##     aln (7831..7884)                                       names
## [1] TGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGT NM_000125.4 Homo ...
## [2] TGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGT XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGT Consensus 
## 
##     aln (7885..7938)                                       names
## [1] TTTGTCGCAGCTTTGCTTTGTTTAATGAAACACACTTGTAAACCTCTTTTGCAC NM_000125.4 Homo ...
## [2] TTTGTCGCAGCTTTGCTTTGTTTAATGAAACACACTTGTAAACCTCTTTTGCAC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTTGTCGCAGCTTTGCTTTGTTTAATGAAACACACTTGTAAACCTCTTTTGCAC Consensus 
## 
##     aln (7939..7992)                                       names
## [1] TTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACC NM_000125.4 Homo ...
## [2] TTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACC XM_009452243.3 PR...
## [3] ------------------------------------------------------ XM_015137107.2 PR...
## Con TTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACC Consensus 
## 
##     aln (7993..8024)                 names
## [1] TATTTGATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
## [2] TATTTGATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
## [3] -------------------------------- XM_015137107.2 PR...
## Con TATTTGATGTTCAAATAAAGAATTAAACTAAA Consensus

Pathway Analysis Since Pathway analysis directly connects to the results of RNA-seq, once the previous coding error unde the RNA-seq data is worked out, pathway analysis will be shown, for now, below is a comment of the skeleton of the input

#go<- goana(tr, species= "Homo Sapien") 
#topGO(go, n=15)